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At least 1,783 records · Page 99

Elucidation of complex respiratory chains: a straightforward strategy to monitor electron transfer between cytochromes

Abstract Cytochromes are electron transfer (ET) proteins essential in various biological systems, playing crucial roles in the respiratory chains of bacteria. These proteins are particularly abundant in electrogenic microorganisms and are responsible for the efficient delivery of electrons to the cells’ exterior. The capability of sending electrons outside the cells open new avenues to be explored for emerging biotechnological applications in bioremediation, microbial electrosynthesis, and bioenergy fields. To develop these applications, it is critical to identify the different redox partners and to elucidate the stepwise ET along the respiratory paths. However, investigating direct ET events between proteins with identical features in nearly all spectroscopic techniques is extremely challenging. Nuclear magnetic resonance (NMR) spectroscopy offers the possibility to overcome this difficulty by analysing the alterations of the spectral signatures of each protein caused by electron exchange events. The uncrowded NMR spectral regions containing the heme resonances of the cytochromes display unique and distinct signatures in the reduced and oxidized states, which can be explored to monitor ET within the redox complex. In this study, we present a strategy for a fast and straightforward monitorization of ET between c-type cytochromes, using as model a triheme periplasmic cytochrome and a membrane-associated monoheme cytochrome from the electrogenic bacterium Geobacter sulfurreducens. The comparison between the 1D 1H NMR spectra obtained for samples containing the two cytochromes and for samples containing the individual proteins clearly demonstrated a unidirectional ET within the redox complex. This strategy provides a simple and straightforward means to elucidate complex biologic respiratory ET chains.

Morgado, Leonor (ORCID:0000000237605180)↗

Solutes that reduce yield strength anisotropies in magnesium from first principles

Using Labusch-type solid solution strengthening models parameterized with DFT-computed solute-dislocation interaction energies, we perform a computational search for 63 solutes across the periodic table to find those that lower anisotropy ratios (non-basal to basal CRSS) of magnesium potentially increasing its ductility per the von Mises criterion. For this purpose, we compute changes in strength for solutes as a function of composition and temperature, and compute anisotropy ratios for solutes that include both rare earth and non-rare earth elements. Here we specifically focus on solute-dislocation interaction energies in the following DFT-optimized dislocations as representative of three non-basal plastic deformation modes: $\langle c + a \rangle$ edge, (10$\bar1$2) tension twinning edge, and the (10$\bar{1}$1) compression twinning edge. We find that solute-induced changes in non-basal deformation modes can be approximated using a second-order polynomial in the size misfit of the solutes, which permits rapid screening of solutes. Our approach to identify solutes known to improve strengthening incorporates solute solubility, and suggests other solutes that not have been previously explored for strengthening. The 8 rare-earth solutes that our method suggests as the best, ordered by increasing anisotropy ratios at their optimal concentrations, are: Gd, Tb, Dy, Nd, Ho, Er, Tm, and Yb. The 12 non-rare-earth solutes that our method suggests as the best, ordered by increasing anisotropy ratios, are: Y, Mn, Sc, Pb, Ca, Ag, Bi, Tl, Zn, Li, Ga, and Al. Of these, Gd, Nd, Er, Yb, Y, Mn, Ca, Zn, Li, and Al are used in commercial Mg alloys.

36 MATERIALS SCIENCE↗

Developing a Distributed Trust Model for Distributed Energy Resources

Electric power system operators can manage distribution system reliability by coordinating end customer usage of distributed energy resources. The end customers in this regard are Service Provisioning Customers, who provide their energy resources to a Grid Service Provider, which in turn dispatches large aggregations of distributed energy resources to provide reliable service to the power system.The security of this system relies upon information protection mechanisms, as described in IEEE 2030.5. However, in addition to preventive security measures, a monitoring function is required to ensure trustworthiness. Trust models are a method to detect and respond to both expected and unexpected behavior. Different trust models are required for various types and characteristics of each situation. This paper will describe the topics that must be considered when developing a trust model as it applies to distributed energy resources. The major contribution of this paper is the creation and application of a Distributed Trust Model applied to distributed energy resources.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Surrogate Distributed Radiological Sources—Part III: Quantitative Distributed Source Reconstructions

In this third part of a multi-paper series, we present quantitative image reconstruction results from aerial measurements of eight different surrogate distributed gamma-ray sources on flat terrain. Here, we show that our quantitative imaging methods can accurately reconstruct the expected shapes, and, after appropriate calibration, the absolute activity of the distributed sources. We conduct several studies of imaging performance versus various measurement and reconstruction parameters, including detector altitude and raster pass spacing, data and modeling fidelity, and regularization type and strength. The imaging quality performance is quantified using various quantitative image quality metrics. Our results confirm the utility of point source arrays as surrogates for truly distributed radiological sources, and advance the quantitative capabilities of Scene Data Fusion gamma-ray imaging methods.

Airborne survey↗

DQ Admittance Model Extraction for IBRs via Gaussian Pulse Excitation

While $dq$ admittance models have shown to be very useful for stability analysis, extracting admittance models of inverter-based resources (IBRs) from the electromagnetic transient (EMT) simulation environment using frequency scans takes time. In this letter, a new perturbation method based on Gaussian pulses in combination with the system identification algorithms shows great promise for parametric $dq$ admittance model extraction. We present the $dq$ admittance model extracting method for a type-4 wind turbine. Challenges in implementing Gaussian pulse excitation are also pointed out. In conclusion, the extracted $dq$ admittance model via the new method shows to have a high matching degree with the measurements obtained from frequency scans.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Canopy tree mortality depends on the proportion of crown exposed to sunlight, but this effect varies with species' wood density

Abstract Understanding what drives changes in tree mortality as well as the covariates influencing trees' response is a research priority to predict forest responses to global change. Here, we combined drone photogrammetry and ground‐based data to assess the influence of crown exposure to light (relative to total crown area), growth deviations (relative to conspecifics), tree size, and species' wood density (as a surrogate for light‐demanding and shade‐tolerant life‐history strategies) on the mortality of 984 canopy trees in an Amazonterra firmeforest. Trees with lower wood density were less prone to die when their proportion of crown was more exposed to sunlight, but this relationship with relative crown exposure weakened and slightly reversed as wood density increased. Trees growing less than their species average had higher mortality, especially when the species' wood density decreased. The role of wood density in determining the survival of canopy trees under varying light conditions indicates differential responses of light‐demanding versus shade‐tolerant species. Our results highlight the importance of accounting for life‐history strategies, via plant functional types, in vegetation dynamic models aiming to predict forest demography under a rapidly changing climate. Abstract in Spanish is available with online material.

Environmental Sciences & Ecology↗

A genoscape–network model for conservation prioritization in a migratory bird

Migratory animals are declining worldwide and coordinated conservation efforts are needed to reverse current trends. We devised a novel genoscape-network model that combines genetic analyses with species distribution modeling and demographic data to overcome challenges with conceptualizing alternative risk factors in migratory species across their full annual cycle. We applied our method to the long distance, Neotropical migratory bird, Wilson's Warbler (Cardellina pusilla). Despite a lack of data from some wintering locations, we demonstrated how the results can be used to help prioritize conservation of breeding and wintering areas. For example, we showed that when genetic, demographic, and network modeling results were considered together it became clear that conservation recommendations will differ depending on whether the goal is to preserve unique genetic lineages or the largest number of birds per unit area. More specifically, if preservation of genetic lineages is the goal, then limited resources should be focused on preserving habitat in the California Sierra, Basin Rockies, or Coastal California, where the 3 most vulnerable genetic lineages breed, or in western Mexico, where 2 of the 3 most vulnerable lineages overwinter. Alternatively, if preservation of the largest number of individuals per unit area is the goal, then limited conservation dollars should be placed in the Pacific Northwest or Central America, where densities are estimated to be the highest. Overall, our results demonstrated the utility of adopting a genetically based network model for integrating multiple types of data across vast geographic scales and better inform conservation decision-making for migratory animals.

60 APPLIED LIFE SCIENCES↗

Biocrust Mosses and Cyanobacteria Exhibit Distinct Carbon Uptake Responses to Variations in Precipitation Amount and Frequency

ABSTRACT Dryland organisms exhibit varied responses to changes in precipitation, including event size, frequency, and soil moisture duration, influencing carbon uptake and reserve management strategies. This principle, central to the pulse‐reserve paradigm, has not been thoroughly evaluated in biological soil crusts (biocrusts), essential primary producers on dryland surfaces. We conducted two experiments to investigate carbon uptake in biocrusts under different precipitation regimes. In the first, we applied a gradient of watering amounts to biocrusts dominated by moss or cyanobacteria, hypothesising distinct pulse‐response strategies. The second experiment extended watering treatments over three months, varying pulse size and frequency. Our results revealed distinct carbon uptake patterns: moss crusts exhibited increased CO 2 uptake with larger, less frequent watering events, whereas cyanobacteria crusts maintained similar carbon uptake across all event sizes. These findings suggest divergent pulse‐response strategies across biocrust types, with implications for modelling dryland carbon dynamics and informing land management under changing precipitation regimes.

Young, Kristina E. [USDA‐ARS Jornada Experimental ↗

Sixteen multiple-amplifier sensing charge-coupled devices and characterization techniques targeting the next generation of astronomical instruments

We present a candidate sensor for future spectroscopic applications, such as a Stage-5 Spectroscopic Survey Experiment or the Habitable Worlds Observatory. This type of charge-coupled device (CCD) sensor features multiple in-line amplifiers at its output stage allowing multiple measurements of the same charge packet, either in each amplifier or in the different amplifiers. Recently, the operation of an eight-amplifier sensor has been experimentally demonstrated, and we present the operation of a 16-amplifier sensor. This new sensor enables a noise level of ∼1 erms− with a single sample per amplifier. In addition, it is shown that sub-electron noise can be achieved using multiple samples per amplifier. In addition to demonstrating the performance of the 16-amplifier sensor, we aim to create a framework for future analysis and performance optimization of this type of detectors. New models and techniques are presented to characterize specific parameters, which are absent in conventional CCDs and Skipper CCDs: charge transfer between amplifiers and independent and common noise in the amplifiers and their processing.

16 multiple-amplifer sensing CCD (MAS-CCD)↗

The secret structure of the gravitational vacuum

We argue that the vacuum of quantum gravity must contain a hierarchical structure of correlations spanning all length scales. These correlated domains (called “vecros”) correspond to virtual fluctuations of black hole microstates. Larger fluctuations are suppressed by their larger action, but this suppression is offset by a correspondingly larger phase space of possible configurations. We give an explicit lattice model of these vecro fluctuations, noting how their distribution changes as the gravitational pull of a star becomes stronger. At the threshold of formation of a closed trapped surface, these virtual fluctuations transition into on-shell black hole microstates (fuzzballs). Fuzzballs radiate from their surface like normal bodies, resolving the information paradox. Here, we also argue that any model without vecro-type extended vacuum correlations cannot resolve the paradox.

79 ASTRONOMY AND ASTROPHYSICS↗

Gamma-ray Spectrum Explanations (GRSE) v0.1

This code repository provides tools for producing various types of machine learning model explanations trained on gamma-ray spectra. It includes implementations of saliency mapping, Grad-CAM, LIME, and Kernel SHAP, including improvements and clarifications to some of the approaches that are specific to their use with gamma-ray spectral data. These tools are in support of the manuscript M.S. Bandstra et al., "Explaining machine-learning models for gamma-ray detection and identification," under review at PLOS ONE.

Bandstra, Mark↗

A deep learning-enhanced framework for multiphysics joint inversion

Joint inversion has drawn considerable attention due to the availability of multiple geophysical data sets, ever-increasing computational resources, the development of advanced algorithms, and its ability to reduce inversion uncertainty. A key issue of joint inversion is to develop effective strategies to link different geophysical data in a unified mathematical framework, in which the information obtained from different models can complement each other. We have developed a deep learning-enhanced joint inversion framework to simultaneously reconstruct different physical models by fusing different types of geophysical data. Traditionally, structure similarity constraints are pursued by joint inversion algorithms using manually crafted formulations (e.g., cross gradient). The constraint is constructed by a deep neural network (DNN) during the learning process. The framework is designed to combine the DNN and a traditional independent inversion workflow and improve the joint inversion result iteratively. The network can be easily extended to incorporate multiphysics without structural changes. Numerical experiments on the joint inversion of 2D DC resistivity data and seismic traveltime are used to validate our method. In addition, this learning-based framework demonstrates excellent generalization abilities when tested on data sets using different geologic structures. It also can handle different sensing configurations and nonconforming discretization.

Geochemistry & Geophysics↗

Covariate Dependent Sparse Functional Data Analysis

This study proposes a method to incorporate covariate information into sparse functional data analysis. The method aims at cases where each subject has a limited number of longitudinal measurements and is associated with static covariates. This research is motivated by several use cases in practice. One representative example is void swelling, a nuclear-specific material degradation mechanism. Void swelling is affected by many covariates, including alloy composition and irradiation type. How to accurately model the complicated joint effects of such covariates on the swelling process is the key to mitigating the effect of swelling and ensuring safe operation. Unlike most of the existing methods, the proposed method can handle high-dimensional covariates with the informative covariate identification procedure and sparse and irregularly spaced measurements, that is, does not require complete or dense observations. The main innovation of the proposed method is that we model the variation coming from covariates and the variation left conditioned on covariates, such that the functional principal component analysis and Gaussian process can be conducted in a unified manner. Further, we also propose a systematic approach to identify important covariates in the hypothesis testing context. The methodology is demonstrated on applications in nuclear engineering and healthcare and simulation studies.

42 ENGINEERING↗

Understanding surfaces and interfaces in nanocomposites of silicone and barium titanate through experiments and modeling

Barium titanate (BTO) is a ferroelectric perovskite used in electronics and energy storage systems because of its high dielectric constant. Decreasing the BTO particle size was shown to increase the dielectric constant of the perovskite, which is an intriguing but contested result. We investigated this result by fabricating silicone-matrix nanocomposite specimens containing BTO particles of decreasing diameter. Furthermore, density functional theory modeling was used to understand the interactions at the BTO particle surface. Combining results from experiments and modeling indicated that polymer type, particle surface interactions, and particle surface structure can influence the dielectric properties of polymer-matrix nanocomposites containing BTO.

composite↗

Initial Implementation Of Machine Learning System for SRF Cavity Fault Classification at CEBAF

The Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Laboratory is high power CW electron accelerator. It uses a mixture of two types of SRF modules, older, lower energy C20/C50 modules and newer higher energy C100 modules, arrayed in two anti-parallel linear accelerators. Accurately classifying the type of cavity faults is essential to maintaining and improving accelerator performance. Each C100 cryomodule contains eight 7-cell cavities. When a cavity fault occurs within a cryomodule, all eight cavities generate 17 waveforms each containing 8192 points. This data is exported from EPICS and saved for review. Analysis of these waveforms is time intensive and requires subject matter expertise (SME). SMEs examine the data from each event and label it according to one of several known cavity fault types. Multiple machine learning models have been developed on this labeled dataset with sufficient performance to warrant the creation of a limited machine learning software system for use by accelerator operations staff. This paper discusses the transition from model development to implementation of a prototype system.

Carpenter, A.↗

XCP- Computational Summer Workshop: Equation of State Overview [Slides]

An overview of Equation of State (EOS) theory, some relevant physics, experiments, computational methods, and the SESAME database will be presented. The goal will be to describe what types of data and modeling are required to make an EOS that typically spans up to ~10 9 GPa in pressure and 10 9 K in temperature.

42 ENGINEERING↗

An unstructured C-grid type variational formulation for the sea ice dynamics

Historically, B-grid formulations of sea ice dynamics have been dominant because they have matched the grid type used by ocean models. The reason for the grid match is simple – it facilitates penetration of the curl of ice-ocean stress into the deep ocean with minimal numerical diffusivity because sea ice and ocean velocity are co-located. In recent years, as ocean models have increasingly progressed to C-grids, sea ice models have followed suit on quadrilateral meshes, but the implementation of an unstructured C-grid sea ice models is new. We present an unstructured C-grid discretization of the Elastic Viscous Plastic (EVP) rheology, where the velocity unknowns are discretized at the edges of the mesh cells with n-sides, where typically n is greater than or equal to four, rather than at the vertices, as in the B-grid. Our framework of choice is the Model for Prediction Across Scales (MPAS) within E3SM, the climate model of the U.S. Department of Energy, although our approach is general and could be applied to other models as well. While MPAS-Seaice is currently defined on a B-grid, MPAS-Ocean runs on a C-grid, hence interpolation operators are heavily used when coupled simulations are performed. In this work, we describe a mathematical formulation to transition the dynamics of MPAS-Seaice to a C-grid, in order to ultimately facilitate the coupling with MPAS-Ocean and reduce numerical errors associated with this communication. Numerical results are reported to highlight the features of the method.

58 GEOSCIENCES↗